9HEO | pdb_00009heo

Open-state RyR1 in 0.05% POPC micelles, in complex with a nanobody and FKBP

PDB DOI: https://doi.org/10.2210/pdb9HEO/pdb
EM Map EMD-52085: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Oryctolagus cuniculus, Lama glama
Expression System: Oryctolagus cuniculus, Escherichia coli
Mutation(s): No

Deposited: 2024-11-14 Released: 2025-09-17
Deposition Author(s): Li, C., Efremov, R.G.
Funding Organization(s): Research Foundation - Flanders (FWO), European Research Council (ERC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Open-state RyR1 in 0.05% POPC micelles, in complex with a nanobody and FKBP

Li, C., Efremov, R.G.

To be published.

Macromolecule Content

Total Structure Weight: 2,419.48 kDa
Atom Count: 146,783
Modeled Residue Count: 18,240
Deposited Residue Count: 21,040
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ryanodine receptor 1	A, C, G, J	5,027	Oryctolagus cuniculus	Mutation(s): 0 Gene Names: RYR1
UniProt
Find proteins for P11716 (Oryctolagus cuniculus) Explore P11716 Go to UniProtKB: P11716
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11716
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 9657	B, D, H, K	126	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1B	E, F, I, L	107	Oryctolagus cuniculus	Mutation(s): 0 Gene Names: FKBP1B, FKBP12.6 EC: 5.2.1.8
UniProt
Find proteins for Q8HYX6 (Oryctolagus cuniculus) Explore Q8HYX6 Go to UniProtKB: Q8HYX6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8HYX6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POV (Subject of Investigation/LOI) Query on POV Download Ideal Coordinates CCD File SDF format, chain ZB [auth G] SDF format, chain ZA [auth C] SDF format, chain Z [auth A] SDF format, chain YB [auth G] SDF format, chain YA [auth C] SDF format, chain Y [auth A] SDF format, chain XB [auth G] SDF format, chain XA [auth C] SDF format, chain X [auth A] SDF format, chain WB [auth G] SDF format, chain WA [auth C] SDF format, chain W [auth A] SDF format, chain VC [auth J] SDF format, chain VB [auth G] SDF format, chain VA [auth C] SDF format, chain V [auth A] SDF format, chain UC [auth J] SDF format, chain UB [auth G] SDF format, chain UA [auth C] SDF format, chain U [auth A] SDF format, chain TC [auth J] SDF format, chain TB [auth G] SDF format, chain TA [auth C] SDF format, chain T [auth A] SDF format, chain SC [auth J] SDF format, chain SB [auth G] SDF format, chain SA [auth C] SDF format, chain S [auth A] SDF format, chain RC [auth J] SDF format, chain RB [auth G] SDF format, chain RA [auth C] SDF format, chain R [auth A] SDF format, chain QC [auth J] SDF format, chain QB [auth G] SDF format, chain QA [auth C] SDF format, chain Q [auth A] SDF format, chain PC [auth J] SDF format, chain PB [auth G] SDF format, chain PA [auth C] SDF format, chain OC [auth J] SDF format, chain OB [auth G] SDF format, chain NC [auth J] SDF format, chain NB [auth G] SDF format, chain MC [auth J] SDF format, chain MB [auth G] SDF format, chain LC [auth J] SDF format, chain LB [auth G] SDF format, chain KA [auth C] SDF format, chain JA [auth C] SDF format, chain IA [auth C] SDF format, chain HA [auth A] SDF format, chain GC [auth J] SDF format, chain GB [auth G] SDF format, chain GA [auth A] SDF format, chain FC [auth J] SDF format, chain FB [auth G] SDF format, chain FA [auth A] SDF format, chain EC [auth J] SDF format, chain EB [auth G] SDF format, chain EA [auth A] SDF format, chain DC [auth J] SDF format, chain DB [auth C] SDF format, chain DA [auth A] SDF format, chain CC [auth J] SDF format, chain CB [auth C] SDF format, chain CA [auth A] SDF format, chain BC [auth J] SDF format, chain BB [auth C] SDF format, chain BA [auth A] SDF format, chain AC [auth J] SDF format, chain AB [auth C] SDF format, chain AA [auth A] MOL2 format, chain ZB [auth G] MOL2 format, chain ZA [auth C] MOL2 format, chain Z [auth A] MOL2 format, chain YB [auth G] MOL2 format, chain YA [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain XB [auth G] MOL2 format, chain XA [auth C] MOL2 format, chain X [auth A] MOL2 format, chain WB [auth G] MOL2 format, chain WA [auth C] MOL2 format, chain W [auth A] MOL2 format, chain VC [auth J] MOL2 format, chain VB [auth G] MOL2 format, chain VA [auth C] MOL2 format, chain V [auth A] MOL2 format, chain UC [auth J] MOL2 format, chain UB [auth G] MOL2 format, chain UA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain TC [auth J] MOL2 format, chain TB [auth G] MOL2 format, chain TA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain SC [auth J] MOL2 format, chain SB [auth G] MOL2 format, chain SA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain RC [auth J] MOL2 format, chain RB [auth G] MOL2 format, chain RA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain QC [auth J] MOL2 format, chain QB [auth G] MOL2 format, chain QA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain PC [auth J] MOL2 format, chain PB [auth G] MOL2 format, chain PA [auth C] MOL2 format, chain OC [auth J] MOL2 format, chain OB [auth G] MOL2 format, chain NC [auth J] MOL2 format, chain NB [auth G] MOL2 format, chain MC [auth J] MOL2 format, chain MB [auth G] MOL2 format, chain LC [auth J] MOL2 format, chain LB [auth G] MOL2 format, chain KA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain HA [auth A] MOL2 format, chain GC [auth J] MOL2 format, chain GB [auth G] MOL2 format, chain GA [auth A] MOL2 format, chain FC [auth J] MOL2 format, chain FB [auth G] MOL2 format, chain FA [auth A] MOL2 format, chain EC [auth J] MOL2 format, chain EB [auth G] MOL2 format, chain EA [auth A] MOL2 format, chain DC [auth J] MOL2 format, chain DB [auth C] MOL2 format, chain DA [auth A] MOL2 format, chain CC [auth J] MOL2 format, chain CB [auth C] MOL2 format, chain CA [auth A] MOL2 format, chain BC [auth J] MOL2 format, chain BB [auth C] MOL2 format, chain BA [auth A] MOL2 format, chain AC [auth J] MOL2 format, chain AB [auth C] MOL2 format, chain AA [auth A] mmCIF format, chain ZB [auth G] mmCIF format, chain ZA [auth C] mmCIF format, chain Z [auth A] mmCIF format, chain YB [auth G] mmCIF format, chain YA [auth C] mmCIF format, chain Y [auth A] mmCIF format, chain XB [auth G] mmCIF format, chain XA [auth C] mmCIF format, chain X [auth A] mmCIF format, chain WB [auth G] mmCIF format, chain WA [auth C] mmCIF format, chain W [auth A] mmCIF format, chain VC [auth J] mmCIF format, chain VB [auth G] mmCIF format, chain VA [auth C] mmCIF format, chain V [auth A] mmCIF format, chain UC [auth J] mmCIF format, chain UB [auth G] mmCIF format, chain UA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain TC [auth J] mmCIF format, chain TB [auth G] mmCIF format, chain TA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain SC [auth J] mmCIF format, chain SB [auth G] mmCIF format, chain SA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain RC [auth J] mmCIF format, chain RB [auth G] mmCIF format, chain RA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain QC [auth J] mmCIF format, chain QB [auth G] mmCIF format, chain QA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain PC [auth J] mmCIF format, chain PB [auth G] mmCIF format, chain PA [auth C] mmCIF format, chain OC [auth J] mmCIF format, chain OB [auth G] mmCIF format, chain NC [auth J] mmCIF format, chain NB [auth G] mmCIF format, chain MC [auth J] mmCIF format, chain MB [auth G] mmCIF format, chain LC [auth J] mmCIF format, chain LB [auth G] mmCIF format, chain KA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain HA [auth A] mmCIF format, chain GC [auth J] mmCIF format, chain GB [auth G] mmCIF format, chain GA [auth A] mmCIF format, chain FC [auth J] mmCIF format, chain FB [auth G] mmCIF format, chain FA [auth A] mmCIF format, chain EC [auth J] mmCIF format, chain EB [auth G] mmCIF format, chain EA [auth A] mmCIF format, chain DC [auth J] mmCIF format, chain DB [auth C] mmCIF format, chain DA [auth A] mmCIF format, chain CC [auth J] mmCIF format, chain CB [auth C] mmCIF format, chain CA [auth A] mmCIF format, chain BC [auth J] mmCIF format, chain BB [auth C] mmCIF format, chain BA [auth A] mmCIF format, chain AC [auth J] mmCIF format, chain AB [auth C] mmCIF format, chain AA [auth A]	AA [auth A] AB [auth C] AC [auth J] BA [auth A] BB [auth C] AA [auth A], AB [auth C], AC [auth J], BA [auth A], BB [auth C], BC [auth J], CA [auth A], CB [auth C], CC [auth J], DA [auth A], DB [auth C], DC [auth J], EA [auth A], EB [auth G], EC [auth J], FA [auth A], FB [auth G], FC [auth J], GA [auth A], GB [auth G], GC [auth J], HA [auth A], IA [auth C], JA [auth C], KA [auth C], LB [auth G], LC [auth J], MB [auth G], MC [auth J], NB [auth G], NC [auth J], OB [auth G], OC [auth J], PA [auth C], PB [auth G], PC [auth J], Q [auth A], QA [auth C], QB [auth G], QC [auth J], R [auth A], RA [auth C], RB [auth G], RC [auth J], S [auth A], SA [auth C], SB [auth G], SC [auth J], T [auth A], TA [auth C], TB [auth G], TC [auth J], U [auth A], UA [auth C], UB [auth G], UC [auth J], V [auth A], VA [auth C], VB [auth G], VC [auth J], W [auth A], WA [auth C], WB [auth G], X [auth A], XA [auth C], XB [auth G], Y [auth A], YA [auth C], YB [auth G], Z [auth A], ZA [auth C], ZB [auth G]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth C] Focus chain AC [auth J] Focus chain BA [auth A] Focus chain BB [auth C] Focus chain BC [auth J] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain CC [auth J] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain DC [auth J] Focus chain EA [auth A] Focus chain EB [auth G] Focus chain EC [auth J] Focus chain FA [auth A] Focus chain FB [auth G] Focus chain FC [auth J] Focus chain GA [auth A] Focus chain GB [auth G] Focus chain GC [auth J] Focus chain HA [auth A] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LB [auth G] Focus chain LC [auth J] Focus chain MB [auth G] Focus chain MC [auth J] Focus chain NB [auth G] Focus chain NC [auth J] Focus chain OB [auth G] Focus chain OC [auth J] Focus chain PA [auth C] Focus chain PB [auth G] Focus chain PC [auth J] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain QB [auth G] Focus chain QC [auth J] Focus chain R [auth A] Focus chain RA [auth C] Focus chain RB [auth G] Focus chain RC [auth J] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SB [auth G] Focus chain SC [auth J] Focus chain T [auth A] Focus chain TA [auth C] Focus chain TB [auth G] Focus chain TC [auth J] Focus chain U [auth A] Focus chain UA [auth C] Focus chain UB [auth G] Focus chain UC [auth J] Focus chain V [auth A] Focus chain VA [auth C] Focus chain VB [auth G] Focus chain VC [auth J] Focus chain W [auth A] Focus chain WA [auth C] Focus chain WB [auth G] Focus chain X [auth A] Focus chain XA [auth C] Focus chain XB [auth G] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain YB [auth G] Focus chain Z [auth A] Focus chain ZA [auth C] Focus chain ZB [auth G] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth C] Focus chain AC [auth J] Focus chain BA [auth A] Focus chain BB [auth C] Focus chain BC [auth J] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain CC [auth J] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain DC [auth J] Focus chain EA [auth A] Focus chain EB [auth G] Focus chain EC [auth J] Focus chain FA [auth A] Focus chain FB [auth G] Focus chain FC [auth J] Focus chain GA [auth A] Focus chain GB [auth G] Focus chain GC [auth J] Focus chain HA [auth A] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LB [auth G] Focus chain LC [auth J] Focus chain MB [auth G] Focus chain MC [auth J] Focus chain NB [auth G] Focus chain NC [auth J] Focus chain OB [auth G] Focus chain OC [auth J] Focus chain PA [auth C] Focus chain PB [auth G] Focus chain PC [auth J] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain QB [auth G] Focus chain QC [auth J] Focus chain R [auth A] Focus chain RA [auth C] Focus chain RB [auth G] Focus chain RC [auth J] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SB [auth G] Focus chain SC [auth J] Focus chain T [auth A] Focus chain TA [auth C] Focus chain TB [auth G] Focus chain TC [auth J] Focus chain U [auth A] Focus chain UA [auth C] Focus chain UB [auth G] Focus chain UC [auth J] Focus chain V [auth A] Focus chain VA [auth C] Focus chain VB [auth G] Focus chain VC [auth J] Focus chain W [auth A] Focus chain WA [auth C] Focus chain WB [auth G] Focus chain X [auth A] Focus chain XA [auth C] Focus chain XB [auth G] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain YB [auth G] Focus chain Z [auth A] Focus chain ZA [auth C] Focus chain ZB [auth G]
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain MA [auth C] SDF format, chain IC [auth J] SDF format, chain IB [auth G] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain IC [auth J] MOL2 format, chain IB [auth G] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain IC [auth J] mmCIF format, chain IB [auth G]	IB [auth G], IC [auth J], MA [auth C], N [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain IB [auth G] Focus chain IC [auth J] Focus chain MA [auth C] Focus chain N [auth A] Interactions & Density Focus chain IB [auth G] Focus chain IC [auth J] Focus chain MA [auth C] Focus chain N [auth A]
CFF (Subject of Investigation/LOI) Query on CFF Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain NA [auth C] SDF format, chain JC [auth J] SDF format, chain JB [auth G] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain JC [auth J] MOL2 format, chain JB [auth G] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain JC [auth J] mmCIF format, chain JB [auth G]	JB [auth G], JC [auth J], NA [auth C], O [auth A]	CAFFEINE C₈ H₁₀ N₄ O₂ RYYVLZVUVIJVGH-UHFFFAOYSA-N		Interactions Focus chain JB [auth G] Focus chain JC [auth J] Focus chain NA [auth C] Focus chain O [auth A] Interactions & Density Focus chain JB [auth G] Focus chain JC [auth J] Focus chain NA [auth C] Focus chain O [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain LA [auth C] SDF format, chain HC [auth J] SDF format, chain HB [auth G] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain HC [auth J] MOL2 format, chain HB [auth G] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain HC [auth J] mmCIF format, chain HB [auth G]	HB [auth G], HC [auth J], LA [auth C], M [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain HB [auth G] Focus chain HC [auth J] Focus chain LA [auth C] Focus chain M [auth A] Interactions & Density Focus chain HB [auth G] Focus chain HC [auth J] Focus chain LA [auth C] Focus chain M [auth A]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain OA [auth C] SDF format, chain KC [auth J] SDF format, chain KB [auth G] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain KC [auth J] MOL2 format, chain KB [auth G] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain KC [auth J] mmCIF format, chain KB [auth G]	KB [auth G], KC [auth J], OA [auth C], P [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain KB [auth G] Focus chain KC [auth J] Focus chain OA [auth C] Focus chain P [auth A] Interactions & Density Focus chain KB [auth G] Focus chain KC [auth J] Focus chain OA [auth C] Focus chain P [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.31

Structure Validation

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Currently 9HEO does not have a validation slider image.

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-17

Deposition Author(s):

Li, C.

Efremov, R.G.

Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	G0H5916N
Research Foundation - Flanders (FWO)	Belgium	G054617N
European Research Council (ERC)	European Union	726436